Predicted secondary structure of the complete 5ʹ end of the 23S rRNA molecule for <i>Scytonema hyalinum</i> HTT-U-KK4.

<p>Type 2 operon is the base structure, and variable bases in the Type 1 operon are shown as alternates. Indels are noted with empty circles where a base was deleted (or an insertion occurred opposite the position). The separation of the first three domains are delineated with lines. Helix 1 consists of the 5ʹ end of the 23S rRNA molecule bound to the 3ʹ end of the molecule, indicated by labels of 5ʹ and 3ʹ. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186393#pone.0186393.g004" target="_blank">Fig 4</a> for the continuation of the structure (i.e., the 3ʹ end).</p

Promoter regions for Type 1 and Type 2 operons.

<p>The -10 (Pribnow Box) and -35 promoter regions are considered to be likely functional if 3–6 nucleotides in each match the consensus sequence. The optional -52 promoter may or may not be functional in these promoter regions.</p

Phylogenetic tree based on 16S rRNA data.

<p>Sequences of the <i>Scytonema hyalinum</i> species cluster were generated using a combination of cloning strategy and PCR with specific primers designed for each of the two divergent operon types (for details see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186393#sec002" target="_blank">Materials and Methods</a>). The clades corresponding to rRNA operon Type 1 and Type 2 are shown in shaded boxes. The operon Type 1 sequences form a long branch in the tree due to high dissimilarity to all available 16S rRNA sequences of cyanobacteria. Circles with numbers inside indicate strains in which both operon types were recovered. The tree is based on Bayesian Inference; branch supports ≥50% are given at the nodes in this shape: Bayesian Inference/Maximum Likelihood/Neighbor-Joining. Asterisks indicate nodes with ≥95% support from all methods.</p

Phylogenetic tree based on multilocus data.

<p>The tree was inferred from a concatenated nucleotide alignment of partial <i>rpo</i>C1, <i>rbc</i>LX, and <i>nif</i>D sequences (for details see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186393#sec002" target="_blank">Materials and methods</a>). The <i>Scytonema hyalinum</i> species cluster (shaded box) forms a monophyletic lineage sister to <i>Brasilonema</i>. Circles indicate strains in which two divergent (polyphyletic) rRNA operon types were detected. The tree is based on Bayesian Inference; branch supports ≥50% are given at the nodes in this shape: Bayesian Inference/Maximum Likelihood/Neighbor-Joining. Asterisks indicate nodes with 100% support from all methods. Strains sequenced in this study are printed in bold font; accession numbers for the three loci for these strains are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186393#pone.0186393.s004" target="_blank">S4 Table</a>.</p

Predicted secondary structure of the complete 3ʹ end of the 23S rRNA molecule for <i>Scytonema hyalinum</i> HTT-U-KK4.

<p>Type 2 operon is the base structure, and variable bases in the Type 1 operon are shown as alternates. Indels are noted with empty circles where a base was deleted (or an insertion occurred opposite the position). The separation of the last three domains are delineated with lines. Helix 1 consists of the 5ʹ end of the 23S rRNA molecule bound to the 3ʹ end of the molecule, indicated by labels of 5ʹ and 3ʹ. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186393#pone.0186393.g003" target="_blank">Fig 3</a> for the continuation of the structure (i.e., the 5ʹ end).</p

Seven new species of <i>Oculatella</i> (Pseudanabaenales, Cyanobacteria): taxonomically recognizing cryptic diversification

<div><p>A total of 27 strains of <i>Oculatella</i> were isolated, characterized and sequenced, and analysed phylogenetically with an additional environmental clone from the Atacama Desert and 10 strains isolated and sequenced by others. The strains were clearly separated based upon phylogenetic analyses conducted with a concatenated alignment of the 16S rRNA and 16S-23S ITS region of the ribosomal operons in the genus <i>Oculatella</i>. Differences in secondary structure of the conserved domains of the ITS region, as well as comparative analysis of P-distance among ITS regions, served to separate the strains into distinct taxonomic units. Seven new species of <i>Oculatella</i> were described, including four from arid to semi-arid soils (<i>O. atacamensis, O. mojaviensis, O. coburnii, O. neakameniensis</i>) and three from more mesic habitats, including a temperate lake (<i>O. hafneriensis</i>), a desert waterfall (<i>O. cataractarum</i>) and a Hawaiian sea cave (<i>O. kauaiensis</i>). The soil forms show statistically significant morphological differences, but the ranges overlap to a degree that they are not diagnosable by morphology, and these four cryptic species are characterized here using molecular characters. The more mesic species, including the type species from Mediterranean hypogea, <i>O. subterranea</i>, are all morphologically distinct from each other and from all four soil taxa. This report is the first to use solely molecular criteria to distinguish cryptic species of cyanobacteria.</p></div

data for distributional analysis

Thallus and dispersal unit sizes of macroalgae used for analyses in the current manuscript

tufA sequences Submission1762279.txt

tufA sequence

SSU sequences Submission1762486.txt

SSU sequence

excel version of isolates from HfwADB for table 2

GPS data for isolates characterized in the surve